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Contact Information
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Research
I am a postdoc in the group of Katherine Pollard in the Gladstone Institutes at the University of California, San Francisco. I recently completed my PhD under Mona Singh in the Computer Science Department and the Lewis-Sigler Institute for Integrative Genomics at Princeton University.
My research is motivated by the desire to understand:
- how genomes evolve over time and encode the programs that regulate life
- how proteins accomplish their astonishing functional diversity and specificity
Differences between related genomes provide a wealth of information about how organisms work. I use comparative genomics approaches to highlight functional elements and examine the development of novel functions.
Proteins perform nearly all of their functions by interacting with other molecules. My work combines techniques from computer science, information theory, and statistics to analyze and predict the amino acid residues invovled in these interactions. This information sheds light on the complex relationship between protein sequence, structure, and function.
For more information, check out my CV.
Publications
- Novel genes exhibit distinct patterns of function acquisition and network integration
Capra JA, Pollard KS, and Singh M.
Submitted.
- Genomics through the lens of next-generation sequencing
Capra JA, Carbonne L, Riesenfeld SJ, and Wall JD.
Genome Biology, 11(6): 306, 2010.
[Paper] - G-quadruplex DNA sequences are evolutionarily conserved and associated with distinct genomic features in Saccharomyces cerevisiae.
Capra JA*, Paeschke K*, Singh M, and Zakian VA.
PLoS Computational Biology, 6(7): e1000861, 2010. * co-first authors
[Paper] - Algorithms for the Identification of Functional Sites in Proteins
Capra JA.
Ph.D. Thesis, Princeton University, June, 2009.
[Thesis] - Predicting Protein Ligand Binding Sites by Combining Evolutionary Sequence Conservation and 3D Structure
Capra JA, Laskowski RA, Thornton JM, Singh M, and Funkhouser TA.
PLoS Computational Biology, 5(12): e1000585, 2009.
[Paper] [Supporting Code and Data] - Characterization and prediction of residues determining protein functional specificity.
Capra JA and Singh M.
Bioinformatics, 24(13): 1473-1480, 2008.
[Paper] [Supporting Code and Data]
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Predicting functionally important residues from sequence conservation.
Capra JA and Singh M.
Bioinformatics, 23(15): 1875-82, 2007.
[Paper] [Supporting Code and Data]
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Informatics center for mouse genomics: the dissection of complex traits of the nervous system.
Rosen GD, La Porte NT, Diechtiareff B, Pung CJ, Nissanov J, Gustafson C, Bertrand L, Gefen S,
Fan Y, Tretiak OJ, Manly KF, Park MR, Williams AG, Connolly MT, Capra JA, Williams RW.
Neuroinformatics, 1(4): 327-42. 2003.
[Paper]
Other Stuff I Like
- We Built This City On Rock & Roll on 103.3 WPRB: Princeton
- Talking about your paper at the Princeton Writing Center
- Cache Hitters Summer Softball
- My buddy Nick's goalkeeper gloves